Awsome build and I also understand why you want that boxer torque feel, its wonderful
As far a small cv joints go you might check into the front axle shafts on 4x4 atvs. I saw cjracer used one in his ktm all wheel drive project that is smallish and might just fit in the factory bmw housing. On the other hand I've only heard of one u-joints failure in a bmw driveline and I would be inclined to just use the factory driveline, just checking the balance of the the driveshaft assembly and making sure the ujoints are in good shape and not abused. Realy looking forward to seeing this come together. Amazing project, all I could ever figure was to hack up an hp2 and make what I needed, this is way beyond that
Going to be a helluva bike!